Impact of the Microbiome on the Human Genome

Humans live in a microbial world that includes pathogenic bacteria, viruses, and fungi that cause lethal infections. In addition, a large number of microbial communities inhabit mucosal surfaces where they provide key metabolic activities, facilitating adaptation to changing environments. New genome technologies enable both sequencing of the human genome and sequence-based cataloging of microbial communities inhabiting human mucosal surfaces. These have revealed intricate two-way relationships between the microbiome and the genome, including strong effects of human genotypes on the composition and activity of the microbiome. Likewise, the microbiome plays an important role in training and regulating the immune system, and acts to modify expression of human genetic risk for debilitating chronic inflammatory and immune conditions. These studies are suggesting a new role of the microbiome in human health and disease.

Public Views on Models for Accessing Genomic and Health Data for Research: Mixed Methods Study

BACKGROUND

The literature abounds with increasing numbers of research studies using genomic data in combination with health data (eg, health records and phenotypic and lifestyle data), with great potential for large-scale research and precision medicine. However, concerns have been raised about social acceptability and risks posed for individuals and their kin. Although there has been public engagement on various aspects of this topic, there is a lack of information about public views on data access models.

OBJECTIVE

This study aimed to address the lack of information on the social acceptability of access models for reusing genomic data collected for research in conjunction with health data. Models considered were open web-based access, released externally to researchers, and access within a data safe haven.

METHODS

Views were ascertained using a series of 8 public workshops (N=116). The workshops included an explanation of benefits and risks in using genomic data with health data, a facilitated discussion, and an exit questionnaire. The resulting quantitative data were analyzed using descriptive and inferential statistics, and the qualitative data were analyzed for emerging themes.

RESULTS

Respondents placed a high value on the reuse of genomic data but raised concerns including data misuse, information governance, and discrimination. They showed a preference for giving consent and use of data within a safe haven over external release or open access. Perceived risks with open access included data being used by unscrupulous parties, with external release included data security, and with safe havens included the need for robust safeguards.

CONCLUSIONS

This is the first known study exploring public views of access models for reusing anonymized genomic and health data in research. It indicated that people are generally amenable but prefer data safe havens because of perceived sensitivities. We recommend that public views be incorporated into guidance on models for the reuse of genomic and health data.

New Human Chromosomal Sites with "Safe Harbor" Potential for Targeted Transgene Insertion

This study identified 35 new sites for targeted transgene insertion that have the potential to serve as new human genomic "safe harbor" sites (SHS). SHS potential for these 35 sites, located on 16 chromosomes, including both arms of the human X chromosome, and for the existing human SHS AAVS1, hROSA26, and CCR5 was assessed using eight different desirable, widely accepted criteria for SHS verifiable with human genomic data. Three representative newly identified sites on human chromosomes 2 and 4 were then experimentally validated by in vitro and in vivo cleavage-sensitivity tests, and analyzed for population-level and cell line-specific sequence variants that might confound site targeting. The highly ranked site on chromosome 4 (SHS231) was further characterized by targeted homology-dependent and -independent transgene insertion and expression in different human cell lines. The structure and fidelity of transgene insertions at this site were confirmed, together with analyses that demonstrated stable expression and function of transgene-encoded proteins, including fluorescent protein markers, selectable marker cassettes, and Cas9 protein variants. SHS-integrated transgene-encoded Cas9 proteins were shown to be capable of introducing a large (17 kb) gRNA-specified deletion in the PAX3/FOXO1 fusion oncogene in human rhabdomyosarcoma cells and as a Cas9-VPR fusion protein to upregulate expression of the muscle-specific transcription factor MYF5 in human rhabdomyosarcoma cells. An engineering "toolkit" was developed to enable easy use of the most extensively characterized of these new human sites, SHS231, located on the proximal long arm of chromosome 4. The target sites identified here have the potential to serve as additional human SHS to enable basic and clinical gene editing and genome-engineering applications.

Genetic variation across the human olfactory receptor repertoire alters odor perception

Humans use a family of more than 400 olfactory receptors (ORs) to detect odors, but there is currently no model that can predict olfactory perception from receptor activity patterns. Genetic variation in human ORs is abundant and alters receptor function, allowing us to examine the relationship between receptor function and perception. We sequenced the OR repertoire in 332 individuals and examined how genetic variation affected 276 olfactory phenotypes, including the perceived intensity and pleasantness of 68 odorants at two concentrations, detection thresholds of three odorants, and general olfactory acuity. Genetic variation in a single OR was frequently associated with changes in odorant perception, and we validated 10 cases in which in vitro OR function correlated with in vivo odorant perception using a functional assay. In 8 of these 10 cases, reduced receptor function was associated with reduced intensity perception. In addition, we used participant genotypes to quantify genetic ancestry and found that, in combination with single OR genotype, age, and gender, we can explain between 10% and 20% of the perceptual variation in 15 olfactory phenotypes, highlighting the importance of single OR genotype, ancestry, and demographic factors in the variation of olfactory perception.

A History of Innovations in the Diagnosis and Treatment of Oral and Head and Neck Cancer

Historical records as far back as 3000 BCE show that oral and head and neck cancer was a disease process well known to Egyptian physicians. Luminaries such as Hippocrates, Galen, Pott, and Virchow were instrumental in shaping our understanding of the etiology and pathogenesis of cancer. During the 20th century, evidence-based medicine catalyzed the development of rigorous science-based diagnostic and treatment protocols. The use of surgery, therapeutic radiation, and chemotherapy as single-treatment agents or in combination with one another gradually emerged as the preferred approach to cancer therapy. The recognition of tobacco, alcohol, and human papillomavirus as etiological agents in oral and head and neck cancer prompted the development of new diagnostic aids and treatment strategies to mitigate cancer progression. More in-depth mechanistic insights into the multistep process of oral and head and neck cancer were made possible by the use of the hamster buccal pouch and mouse models. New technologies, such as the sequencing of the human genome, metabolomics, and proteomics, have provided the foundation for what we today call precision medicine. The future success of tailored medical treatment for cancer patients will depend on the discovery of new druggable targets with improved therapeutic efficacy. As the precision and sensitivity of existing tools for prevention and risk assessment improve, greater accuracy will be achieved in predicting health outcomes.

Genome-wide de novo L1 Retrotransposition Connects Endonuclease Activity with Replication

L1 retrotransposon-derived sequences comprise approximately 17% of the human genome. Darwinian selective pressures alter L1 genomic distributions during evolution, confounding the ability to determine initial L1 integration preferences. Here, we generated high-confidence datasets of greater than 88,000 engineered L1 insertions in human cell lines that act as proxies for cells that accommodate retrotransposition in vivo. Comparing these insertions to a null model, in which L1 endonuclease activity is the sole determinant dictating L1 integration preferences, demonstrated that L1 insertions are not significantly enriched in genes, transcribed regions, or open chromatin. By comparison, we provide compelling evidence that the L1 endonuclease disproportionately cleaves predominant lagging strand DNA replication templates, while lagging strand 3'-hydroxyl groups may prime endonuclease-independent L1 retrotransposition in a Fanconi anemia cell line. Thus, acquisition of an endonuclease domain, in conjunction with the ability to integrate into replicating DNA, allowed L1 to become an autonomous, interspersed retrotransposon.

[A Pipeline for the Error-free Identification of Somatic Alu Insertions in High-throughput Sequencing Data]

Retroelements are considered as one of the important sources of genomic variability in modern humans. It is known that transposition activity of retroelements in germline cells generates new insertions in various genomic loci and sometimes results in genetic diseases. Retroelements activity in somatic cells is restricted by different cellular mechanisms; however, there is an evidence for it in some tissue types. Somatic insertions can trigger tumorigenesis or participate in normal functioning such as generation of neurons' plasticity. In spite of the rapid development of high-throughput sequencing methods a confident detection of somatic insertions is still quite a challenging task. That, in part, is due to the absence of adequate bioinformatic tools for the analysis of sequencing data. Here, we propose an advanced computational pipeline for the identification of somatic insertions in datasets generated by selective amplification and high-throughput sequencing of genomic regions flanking insertions of AluYa5. Particular attention is paid for the identification of various artifacts arising in course of library preparation and the parameters for their filtration. Pipeline sensitivity is confirmed by in silico experiments with artificial datasets. Using the proposed pipeline we remove at least 80% of artifacts and preserve 75% of potentially somatic insertions. The approaches used in this work can be applied for the study of other mobile elements insertion variability.

Artificial Restriction DNA Cutter Using Nuclease S1 for Site-Selective Scission of Genomic DNA

By combining a pair of pseudo-complementary peptide nucleic acids (pcPNAs) with S1 nuclease, a novel tool to cut DNA at a predetermined site can be obtained. Complementary pcPNAs invade the DNA duplex and base pair to each strand of a target site, creating single-stranded regions that are cleaved by S1 nuclease. The scission site can be freely modulated by the design of pcPNAs. This method can be used to cleave a single site in the human genome. This protocol presents experimental details for site-selective scission using this versatile new tool. © 2019 by John Wiley & Sons, Inc.

Human Genome-Edited Babies: First Responder with Concerns Regarding Possible Neurological Deficits!

The ultimate outcome in genome-editing research stepped into unknown territories last month when two babies were brought into the world with clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) facilitated knockdown of chemokine receptor 5 (CCR5). An immediate outcry by the public and the scientific community followed, which is still ongoing with much apprehensions and criticism of the ethical and scientific aspects of the procedure and its effects on the future of genome editing needed in other stubborn inheritable diseases for which there is no cure at present. With the debate on the consequences of this particular receptor knockdown still going on and the after-shocks in the form of queries expected to continue for some time in the future, we enter the arena of this particular genome editing as first responders with concerns regarding the neurological aftermath of CCR5 knockout in the babies born.

Pathways to disease from natural variations in human cytoplasmic tRNAs

Perfectly accurate translation of mRNA into protein is not a prerequisite for life. Resulting from errors in protein synthesis, mistranslation occurs in all cells, including human cells. The human genome encodes >600 tRNA genes, providing both the raw material for genetic variation and a buffer to ensure that resulting translation errors occur at tolerable levels. On the basis of data from the 1000 Genomes Project, we highlight the unanticipated prevalence of mistranslating tRNA variants in the human population and review studies on synthetic and natural tRNA mutations that cause mistranslation or de-regulate protein synthesis. Although mitochondrial tRNA variants are well known to drive human diseases, including developmental disorders, few studies have revealed a role for human cytoplasmic tRNA mutants in disease. In the context of the unexpectedly large number of tRNA variants in the human population, the emerging literature suggests that human diseases may be affected by natural tRNA variants that cause mistranslation or de-regulate tRNA expression and nucleotide modification. This review highlights examples relevant to genetic disorders, cancer, and neurodegeneration in which cytoplasmic tRNA variants directly cause or exacerbate disease and disease-linked phenotypes in cells, animal models, and humans. In the near future, tRNAs may be recognized as useful genetic markers to predict the onset or severity of human disease.

Repetitive Fragile Sites: Centromere Satellite DNA As a Source of Genome Instability in Human Diseases

Maintenance of an intact genome is essential for cellular and organismal homeostasis. The centromere is a specialized chromosomal locus required for faithful genome inheritance at each round of cell division. Human centromeres are composed of large tandem arrays of repetitive alpha-satellite DNA, which are often sites of aberrant rearrangements that may lead to chromosome fusions and genetic abnormalities. While the centromere has an essential role in chromosome segregation during mitosis, the long and repetitive nature of the highly identical repeats has greatly hindered in-depth genetic studies, and complete annotation of all human centromeres is still lacking. Here, we review our current understanding of human centromere genetics and epigenetics as well as recent investigations into the role of centromere DNA in disease, with a special focus on cancer, aging, and human immunodeficiency⁻centromeric instability⁻facial anomalies (ICF) syndrome. We also highlight the causes and consequences of genomic instability at these large repetitive arrays and describe the possible sources of centromere fragility. The novel connection between alpha-satellite DNA instability and human pathological conditions emphasizes the importance of obtaining a truly complete human genome assembly and accelerating our understanding of centromere repeats' role in physiology and beyond.

Retrotransposon insertion as a novel mutational event in Bardet-Biedl syndrome

Background

Bardet‐Biedl syndrome (BBS) is an autosomal recessive pleiotropic disorder of the primary cilia that leads to severe visual loss in the teenage years. Approximately 80% of BBS cases are explained by mutations in one of the 21 identified genes. Documented causative mutation types include missense, nonsense, copy number variation (CNV), frameshift deletions or insertions, and splicing variants.

Methods

Whole genome sequencing was performed on a patient affected with BBS for whom no mutations were identified using clinically approved genetic testing of the known genes. Analysis of the WGS was done using internal protocols and publicly available algorithms. The phenotype was defined by retrospective chart review.

Results

We document a female affected with BBS carrying the most common BBS1 mutation (BBS1: Met390Arg) on the maternal allele and an insertion of a ~1.7‐kb retrotransposon in exon 13 on the paternal allele. This retrotransposon insertion was not automatically annotated by the standard variant calling protocols used. This novel variant was identified by visual inspection of the alignment file followed by specific genome analysis with an available algorithm for transposable elements.

Conclusion

This report documents a novel mutation type associated with BBS and highlights the importance of systematically performing transposon detection analysis on WGS data of unsolved cases.

Infectious Disease and the Diversification of the Human Genome

The human immune system is under great pathogen-mediated selective pressure. Divergent infectious disease pathogenesis across human populations combined with the overrepresentation of "immune genes" in genomic regions with signatures of positive selection suggests that pathogens have significantly altered the human genome. However, important features of the human immune system can confound searches for and interpretations of signatures of pathogen-mediated evolution. Immune system redundancy, immune gene pleiotropy, host ability to acquire immunity and alter the immune repertoire of offspring through "priming," and host microbiome complicate evolutionary interpretations of host-pathogen interactions. The overall promiscuity and sensitivity of the immune system to local environments can also muddy assumptions about the origins of a selective pressure on a given set of genes. This review addresses (a) how features of the immune system, the primary buffer between a pathogen and the human genome, affect evolutionary signal and (b) the considerations that must be made when assessing how pathogens have contributed to human diversification.

Benchmarking computational tools for polymorphic transposable element detection

Transposable elements (TEs) are an important source of human genetic variation with demonstrable effects on phenotype. Recently, a number of computational methods for the detection of polymorphic TE (polyTE) insertion sites from next-generation sequence data have been developed. The use of such tools will become increasingly important as the pace of human genome sequencing accelerates. For this report, we performed a comparative benchmarking and validation analysis of polyTE detection tools in an effort to inform their selection and use by the TE research community. We analyzed a core set of seven tools with respect to ease of use and accessibility, polyTE detection performance and runtime parameters. An experimentally validated set of 893 human polyTE insertions was used for this purpose, along with a series of simulated data sets that allowed us to assess the impact of sequence coverage on tool performance. The recently developed tool MELT showed the best overall performance followed by Mobster and then RetroSeq. PolyTE detection tools can best detect Alu insertion events in the human genome with reduced reliability for L1 insertions and substantially lowered performance for SVA insertions. We also show evidence that different polyTE detection tools are complementary with respect to their ability to detect a complete set of insertion events. Accordingly, a combined approach, coupled with manual inspection of individual results, may yield the best overall performance. In addition to the benchmarking results, we also provide notes on tool installation and usage as well as suggestions for future polyTE detection algorithm development.

Human Suicide Risk and Treatment Study

INTRODUCTION

Suicide is still a major event of human mortality worldwide. Yet human suicide prediction, prevention and therapeutic systems at this moment are generally ineffective in the clinic. No diagnostic system is reliable for significantly suicidal prevention and mortality reduction. As a result, human suicide etiopathologic investigation (especially at genetic/molecular levels in the clinical settings) is quite necessary. In order to boost human suicide researches, emerging human suicide diagnostic/treatment study will be transformed from clinical symptom observations into new generations of candidate drug targets and therapeutics. To achieve this goal, associations between suicidal etiopathologic identification, genetic/bioinformatics-based diagnostics and putative drug targets must be exploited than ever before. After all, the interaction and relationships between environmental/ genetic/molecular clues and overall patient's risk prediction (environmental influences and different therapeutic targets/types) should be found out.

CONCLUSION

In the future, effective clinical suicide prediction, prevention and therapeutic systems can be established via scientific expeditions and causality discovery.

N6-Methyladenine DNA Modification in the Human Genome

DNA N⁶-methyladenine (6mA) modification is the most prevalent DNA modification in prokaryotes, but whether it exists in human cells and whether it plays a role in human diseases remain enigmatic. Here, we showed that 6mA is extensively present in the human genome, and we cataloged 881,240 6mA sites accounting for ∼0.051% of the total adenines. [G/C]AGG[C/T] was the most significantly associated motif with 6mA modification. 6mA sites were enriched in the coding regions and mark actively transcribed genes in human cells. DNA 6mA and N⁶-demethyladenine modification in the human genome were mediated by methyltransferase N6AMT1 and demethylase ALKBH1, respectively. The abundance of 6mA was significantly lower in cancers, accompanied by decreased N6AMT1 and increased ALKBH1 levels, and downregulation of 6mA modification levels promoted tumorigenesis. Collectively, our results demonstrate that DNA 6mA modification is extensively present in human cells and the decrease of genomic DNA 6mA promotes human tumorigenesis.

Detection of HERV-K6 and HERV-K11 transpositions in the human genome

Mobile genetic elements classed as transposons comprise an estimated 45% of the human genome, and 8% of these elements are human endogenous retroviruses (HERVs). Endogenous retroviruses are retrotransposons, containing 5' and 3' long terminal repeat sequences and encoding envelope, group-specific antigen and DNA polymerase proteins. The aim of the present study was to analyse genome integration polymorphisms of HERV type K member 6 (HERV-K6) and HERV-K11 by using the retrotransposon based molecular marker technique, inter-retrotransposon amplified polymorphism (IRAP). For this purpose, blood samples of 18 healthy individuals within the age range of 10-79 years (10 females and 8 males) were collected, genomic DNAs were isolated and IRAP-polymerase chain reaction (PCR) was performed. IRAP-PCR analyses demonstrated that there were 0-70% polymorphism rates for HERV-K6, and 0-38% polymorphism rates for HERV-K11 among all the samples. Furthermore, the polymorphism rates were 0-70% among females and 11-60% among males for HERV-K6, and 0-38% among females and 0-25% among males for HERV-K11. Age-associated polymorphism was also investigated, but no age-associated polymorphism was observed among the samples. Therefore, HERV-K6 and HERV-K11 polymorphisms may arise on an individual-specific basis. Various previous studies have investigated the associations between the expression of HERVs and cancer or other major diseases. However, few reports have analysed HERV-K movements among individuals. This is the first report to investigate HERV-K6 and HERV-K11 retrotransposon polymorphisms between the genders and different age groups.

An Upper Limit on the Functional Fraction of the Human Genome

For the human population to maintain a constant size from generation to generation, an increase in fertility must compensate for the reduction in the mean fitness of the population caused, among others, by deleterious mutations. The required increase in fertility due to this mutational load depends on the number of sites in the genome that are functional, the mutation rate, and the fraction of deleterious mutations among all mutations in functional regions. These dependencies and the fact that there exists a maximum tolerable replacement level fertility can be used to put an upper limit on the fraction of the human genome that can be functional. Mutational load considerations lead to the conclusion that the functional fraction within the human genome cannot exceed 15%.

Human Germline Genome Editing

With CRISPR/Cas9 and other genome-editing technologies, successful somatic and germline genome editing are becoming feasible. To respond, an American Society of Human Genetics (ASHG) workgroup developed this position statement, which was approved by the ASHG Board in March 2017. The workgroup included representatives from the UK Association of Genetic Nurses and Counsellors, Canadian Association of Genetic Counsellors, International Genetic Epidemiology Society, and US National Society of Genetic Counselors. These groups, as well as the American Society for Reproductive Medicine, Asia Pacific Society of Human Genetics, British Society for Genetic Medicine, Human Genetics Society of Australasia, Professional Society of Genetic Counselors in Asia, and Southern African Society for Human Genetics, endorsed the final statement. The statement includes the following positions. (1) At this time, given the nature and number of unanswered scientific, ethical, and policy questions, it is inappropriate to perform germline gene editing that culminates in human pregnancy. (2) Currently, there is no reason to prohibit in vitro germline genome editing on human embryos and gametes, with appropriate oversight and consent from donors, to facilitate research on the possible future clinical applications of gene editing. There should be no prohibition on making public funds available to support this research. (3) Future clinical application of human germline genome editing should not proceed unless, at a minimum, there is (a) a compelling medical rationale, (b) an evidence base that supports its clinical use, (c) an ethical justification, and (d) a transparent public process to solicit and incorporate stakeholder input.

Genomic properties of chromosomal bands are linked to evolutionary rearrangements and new centromere formation in primates

Chromosomal rearrangements in humans are largely related to pathological conditions, and phenotypic effects are also linked to alterations in the expression profile following nuclear relocation of genes between functionally different compartments, generally occupying the periphery or the inner part of the cell nuclei. On the other hand, during evolution, chromosomal rearrangements may occur apparently without damaging phenotypic effects and are visible in currently phylogenetically related species. To increase our insight into chromosomal reorganisation in the cell nucleus, we analysed 18 chromosomal regions endowed with different genomic properties in cell lines derived from eight primate species covering the entire evolutionary tree. We show that homologous loci, in spite of their evolutionary relocation along the chromosomes, generally remain localised to the same functional compartment of the cell nuclei. We conclude that evolutionarily successful chromosomal rearrangements are those that leave the nuclear position of the regions involved unchanged. On the contrary, in pathological situations, the effect typically observed is on gene structure alteration or gene nuclear reposition. Moreover, our data indicate that new centromere formation could potentially occur everywhere in the chromosomes, but only those emerging in very GC-poor/gene-poor regions, generally located in the nuclear periphery, have a high probability of being retained through evolution. This suggests that, in the cell nucleus of related species, evolutionary chromosomal reshufflings or new centromere formation does not alter the functionality of the regions involved or the interactions between different loci, thus preserving the expression pattern of orthologous genes.

Dynamic maps of UV damage formation and repair for the human genome

Formation and repair of UV-induced DNA damage in human cells are affected by cellular context. To study factors influencing damage formation and repair genome-wide, we developed a highly sensitive single-nucleotide resolution damage mapping method [high-sensitivity damage sequencing (HS-Damage-seq)]. Damage maps of both cyclobutane pyrimidine dimers (CPDs) and pyrimidine-pyrimidone (6-4) photoproducts [(6-4)PPs] from UV-irradiated cellular and naked DNA revealed that the effect of transcription factor binding on bulky adducts formation varies, depending on the specific transcription factor, damage type, and strand. We also generated time-resolved UV damage maps of both CPDs and (6-4)PPs by HS-Damage-seq and compared them to the complementary repair maps of the human genome obtained by excision repair sequencing to gain insight into factors that affect UV-induced DNA damage and repair and ultimately UV carcinogenesis. The combination of the two methods revealed that, whereas UV-induced damage is virtually uniform throughout the genome, repair is affected by chromatin states, transcription, and transcription factor binding, in a manner that depends on the type of DNA damage.

The price of whole-genome sequencing may be decreasing, but who will be sequenced?

AIM

Since whole-genome sequencing (WGS) information can have positive and negative personal utility for individuals, we examined predictors of willingness to pay (WTP) for WGS.

PATIENTS & METHODS

We surveyed two independent populations: adult patients (n = 203) and college seniors (n = 980). Ordinal logistic regression models were used to characterize the relationship between predictors and WTP.

RESULTS

Sex, age, education, income, genomic knowledge and knowing someone who had genetic testing or having had genetic testing done personally were associated with significantly higher WTP for WGS. After controlling for income and education, males were willing to pay more for WGS than females.

CONCLUSION

Differences in WTP may impact equity, coverage, affordability and access, and should be anticipated by public dialog about related health policy.

Last rolls of the yoyo: Assessing the human canonical protein count

In 2004, when the protein estimate from the finished human genome was only 24,000, the surprise was compounded as reviewed estimates fell to 19,000 by 2014. However, variability in the total canonical protein counts (i.e. excluding alternative splice forms) of open reading frames (ORFs) in different annotation portals persists. This work assesses these differences and possible causes. A 16-year analysis of Ensembl and UniProtKB/Swiss-Prot shows convergence to a protein number of ~20,000. The former had shown some yo-yoing, but both have now plateaued. Nine major annotation portals, reviewed at the beginning of 2017, gave a spread of counts from 21,819 down to 18,891. The 4-way cross-reference concordance (within UniProt) between Ensembl, Swiss-Prot, Entrez Gene and the Human Gene Nomenclature Committee (HGNC) drops to 18,690, indicating methodological differences in protein definitions and experimental existence support between sources. The Swiss-Prot and neXtProt evidence criteria include mass spectrometry peptide verification and also cross-references for antibody detection from the Human Protein Atlas. Notwithstanding, hundreds of Swiss-Prot entries are classified as non-coding biotypes by HGNC. The only inference that protein numbers might still rise comes from numerous reports of small ORF (smORF) discovery. However, while there have been recent cases of protein verifications from previous miss-annotation of non-coding RNA, very few have passed the Swiss-Prot curation and genome annotation thresholds. The post-genomic era has seen both advances in data generation and improvements in the human reference assembly. Notwithstanding, current numbers, while persistently discordant, show that the earlier yo-yoing has largely ceased. Given the importance to biology and biomedicine of defining the canonical human proteome, the task will need more collaborative inter-source curation combined with broader and deeper experimental confirmation in vivo and in vitro of proteins predicted in silico. The eventual closure could be well be below ~19,000.

What are people willing to pay for whole-genome sequencing information, and who decides what they receive?

PURPOSE

Whole-genome sequencing (WGS) can be used as a powerful diagnostic tool as well as for screening, but it may lead to anxiety, unnecessary testing, and overtreatment. Current guidelines suggest reporting clinically actionable secondary findings when diagnostic testing is performed. We examined preferences for receiving WGS results.

METHODS

A US nationally representative survey (n = 410 adults) was used to rank preferences for who decides (an expert panel, your doctor, you) which WGS results are reported. We estimated the value of information about variants with varying levels of clinical usefulness by using willingness to pay contingent valuation questions.

RESULTS

The results were as follows: 43% preferred to decide themselves what information is included in the WGS report. 38% (95% confidence interval (CI): 33-43%) would not pay for actionable variants, and 3% (95% CI: 1-5%) would pay more than $1,000. 55% (95% CI: 50-60%) would not pay for variants for which medical treatment is currently unclear, and 7% (95% CI: 5-9%) would pay more than $400.

CONCLUSION

Most people prefer to decide what WGS results are reported. Despite valuing actionable information more, some respondents perceive that genetic information could negatively impact them. Preference heterogeneity for WGS information should be considered in the development of policies, particularly to integrate patient preferences with personalized medicine and shared decision making.Genet Med 18 12, 1295-1302.

Challenges and Opportunities of Big Data in Health Care: A Systematic Review

Background

Big data analytics offers promise in many business sectors, and health care is looking at big data to provide answers to many age-related issues, particularly dementia and chronic disease management.

Objective

The purpose of this review was to summarize the challenges faced by big data analytics and the opportunities that big data opens in health care.

Methods

A total of 3 searches were performed for publications between January 1, 2010 and January 1, 2016 (PubMed/MEDLINE, CINAHL, and Google Scholar), and an assessment was made on content germane to big data in health care. From the results of the searches in research databases and Google Scholar (N=28), the authors summarized content and identified 9 and 14 themes under the categories Challenges and Opportunities, respectively. We rank-ordered and analyzed the themes based on the frequency of occurrence.

Results

The top challenges were issues of data structure, security, data standardization, storage and transfers, and managerial skills such as data governance. The top opportunities revealed were quality improvement, population management and health, early detection of disease, data quality, structure, and accessibility, improved decision making, and cost reduction.

Conclusions

Big data analytics has the potential for positive impact and global implications; however, it must overcome some legitimate obstacles.